Question

Which of the following doesn’t describe PAM matrices?

(a) This family of matrices lists the likelihood of change from one amino acid to another in homologous protein sequences during evolution

(b) There is presently no other type of scoring matrix that is based on such sound evolutionary principles as are these matrices

(c) Even though they were originally based on a relatively small data set, the PAM matrices remain a useful tool for sequence alignment

(d) It stands for Percent Altered Mutation

I had been asked this question during an interview for a job.

My question is taken from Use of Scoring Matrices and Gap Penalties in Sequence Alignments topic in portion Sequence Alignment of Bioinformatics

Answer 1

Right option is (d) It stands for Percent Altered Mutation

Easy explanation: PAM stands for Percent Accepted Mutation. In this, each matrix gives the changes expected for a given period of evolutionary time, evidenced by decreased sequence similarity as genes encoding the same protein diverge with increased evolutionary time.